5APG

Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from Vulcanisaeta distributa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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Literature

Ribosome Biogenesis Factor Tsr3 is the Aminocarboxypropyl Transferase Responsible for 18S Rrna Hypermodification in Yeast and Humans

Entian, K.-D.Immer, C.Koetter, P.Lafontaine, D.Britter, M.Pogoryelov, D.Sharma, S.Wohnert, J.Wurm, J.P.

(2016) Nucleic Acids Res 44: 4304

  • DOI: https://doi.org/10.1093/nar/gkw244
  • Primary Citation of Related Structures:  
    5AP8, 5APG

  • PubMed Abstract: 

    The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m(1)acp(3)Ψ) located next to the P-site tRNA on the small subunit 18S rRNA. While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive. Here we identify the cytoplasmic ribosome biogenesis protein Tsr3 as the responsible enzyme in yeast and human cells. In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation. The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode. This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate. Structurally, Tsr3 therefore represents a novel class of acp transferase enzymes.


  • Organizational Affiliation

    Institute for Molecular Biosciences, Goethe University, Frankfurt/M, Germany entian@bio.uni-frankfurt.de.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TSR3
A, B, C
185Vulcanisaeta distributa DSM 14429Mutation(s): 0 
EC: 2.5.1
UniProt
Find proteins for E1QU22 (Vulcanisaeta distributa (strain DSM 14429 / JCM 11212 / NBRC 100878 / IC-017))
Explore E1QU22 
Go to UniProtKB:  E1QU22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1QU22
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.95α = 90
b = 66.97β = 89.99
c = 106.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references